Low-Pass Genome Sequencing for Absence of Heterozygosity Detection
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Solution Overview
Problem
Current methods for detecting absence of heterozygosity (AOH) are limited by the need for high-cost genome sequencing and are not effective with low-pass genome sequencing, which cannot accurately identify AOH or uniparental heterodisomy.
Innovation Solution
A method involving low-pass genome sequencing that aligns sequence reads to a human genome reference, identifies single-nucleotide variants, and determines the rates of homozygous and heterozygous SNVs across windows, allowing for the detection of AOH by comparing these rates to control populations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If low-pass genome sequencing is used, then cost is reduced, but detection accuracy of AOH is insufficient
Solution Approach 1:
The patent changes the analytical parameters by shifting from copy-number-based detection to heterozygous SNP rate-based detection. By calculating the rate of heterozygous SNPs in sliding windows and comparing to control populations, the method achieves accurate AOH detection with low-pass sequencing data that has insufficient individual variant calling precision
Solution Approach 2:
The patent introduces an intermediary approach by using heterozygous SNP rates as a mediator between low-pass sequencing data and AOH detection. Instead of directly detecting AOH from individual variants, the method uses the aggregate heterozygous SNP rate across windows as an intermediate metric that reliably indicates AOH regions
2Measurement precision
If traditional chromosomal microarray analysis is used, then AOH detection is achieved, but resolution is limited to >5-Mb
Solution Approach 1:
The patent makes the low-pass genome sequencing method multi-functional by enabling it to perform both copy-number variant detection and AOH detection through different analytical approaches. The same sequencing data can be analyzed using either read-depth for CNVs or heterozygous SNP rates for AOH, eliminating the need for specialized microarray probes
Solution Approach 2:
The patent transitions from the traditional one-dimensional approach of microarray probe hybridization signals to a two-dimensional analysis by examining both the rate of heterozygous SNPs and the physical window position across the genome. This dimensional expansion enables higher resolution detection by capturing spatial patterns of heterozygosity
3Reliability
If high-coverage genome sequencing is used, then detection sensitivity is improved, but cost increases significantly
Solution Approach 1:
The patent applies partial action by using only the necessary minimum sequencing depth (low-pass) to achieve the detection goal. By analyzing heterozygous SNP rates rather than requiring complete variant calling, the method achieves adequate detection sensitivity with substantially reduced sequencing depth compared to high-coverage requirements
Solution Approach 2:
The patent enables the low-pass sequencing data to serve itself by designing an analysis method that is optimized for low-coverage characteristics. The heterozygous SNP rate approach is inherently suited to low-pass data where individual variant calling is unreliable, allowing the data to be used effectively without requiring additional sequencing
Data Source
AI summary
The present application provides methods of detecting absence of heterozygosity (AOH) in a biological sample from a subject, and computer readable mediums and devices for carrying out the methods.